The short answer is that stomach acid denaturing the digestive enzymes you take is a myth. This was from Dr. Brian Clement, Director of Hippocrates Health Institute.
The companies that produce the enzymes have tagged them and that research is available from companies like National Enzymes where they actually show what it is at ingestion and show what it is at fecal release.
The old paradigm in science teaches us that the stomach acid destroys the digestive enzymes. But the truth is they enter the body as soon as you start to chew them. They go through the stomach, these electrically charged proteins literally enter through ventricles into the blood system and the blood stream throughout the entire process of release.
Furthermore, these electrical proteins in great part go through the digestive fluids, the stomach acids as we call them and are certainly proven to show they’ve done that by the fact that when you test the fecal matter they’re there, or in great part they’re there.
In other words, these studies have shown the presence of the digestive enzymes, not denatured or destroyed, in the fecal matter. Therefore we know the stomach acid did not destroy them.

